Variant report

Variant	rs28410377
Chromosome Location	chr4:144299332-144299333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr4:144298799-144299366	GM12878	blood:	n/a	chr4:144298997-144299011
2	SPI1	chr4:144298524-144299477	GM12878	blood:	n/a	n/a
3	NFIC	chr4:144298652-144299437	GM12878	blood:	n/a	n/a
4	EBF1	chr4:144298342-144299408	GM12878	blood:	n/a	n/a
5	CHD1	chr4:144298552-144299492	GM12878	blood:	n/a	n/a
6	MEF2C	chr4:144298618-144299359	GM12878	blood:	n/a	chr4:144299036-144299057 chr4:144299037-144299053 chr4:144299039-144299054 chr4:144299037-144299054 chr4:144299040-144299051 chr4:144299037-144299052 chr4:144298707-144298722 chr4:144299038-144299052 chr4:144299036-144299057 chr4:144299038-144299053 chr4:144299041-144299050 chr4:144299037-144299052
7	TBP	chr4:144298322-144299335	GM12878	blood:	n/a	n/a
8	RCOR1	chr4:144298828-144299560	GM12878	blood:	n/a	n/a
9	MEF2A	chr4:144298700-144299353	GM12878	blood:	n/a	chr4:144299036-144299057 chr4:144299037-144299053 chr4:144299039-144299054 chr4:144299037-144299054 chr4:144299040-144299051 chr4:144299037-144299052 chr4:144298707-144298722 chr4:144299038-144299052 chr4:144299036-144299057 chr4:144299038-144299053 chr4:144299041-144299050 chr4:144299037-144299052
10	EP300	chr4:144298662-144299417	GM12878	blood:	n/a	chr4:144298997-144299011
11	TBL1XR1	chr4:144298783-144299426	GM12878	blood:	n/a	n/a
12	RUNX3	chr4:144298619-144299341	GM12878	blood:	n/a	n/a
13	STAT5A	chr4:144298714-144299373	GM12878	blood:	n/a	n/a
14	EP300	chr4:144298422-144299405	GM12878	blood:	n/a	chr4:144298997-144299011
15	ATF2	chr4:144298635-144299351	GM12878	blood:	n/a	n/a
16	MXI1	chr4:144298557-144299498	GM12878	blood:	n/a	n/a
17	USF2	chr4:144298961-144299541	GM12878	blood:	n/a	n/a
18	FOXM1	chr4:144298580-144299417	GM12878	blood:	n/a	n/a
19	NFIC	chr4:144298357-144300121	GM12878	blood:	n/a	n/a
20	CHD2	chr4:144298791-144299720	GM12878	blood:	n/a	n/a
21	RELA	chr4:144298553-144299834	GM12878	blood:	n/a	chr4:144298843-144298852 chr4:144298843-144298852
22	ATF2	chr4:144298593-144299412	GM12878	blood:	n/a	n/a
23	NFATC1	chr4:144298713-144299446	GM12878	blood:	n/a	n/a
24	CREB1	chr4:144298594-144299403	GM12878	blood:	n/a	n/a
25	PML	chr4:144298592-144299428	GM12878	blood:	n/a	n/a
26	FOXM1	chr4:144298608-144299355	GM12878	blood:	n/a	n/a
27	MTA3	chr4:144298630-144299424	GM12878	blood:	n/a	n/a
28	NFATC1	chr4:144298797-144299378	GM12878	blood:	n/a	n/a
29	RELA	chr4:144298531-144299420	GM19099	blood:	n/a	chr4:144298843-144298852 chr4:144298843-144298852
30	BCLAF1	chr4:144298700-144299448	GM12878	blood:	n/a	chr4:144299002-144299011 chr4:144298844-144298853

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:144254627..144258395-chr4:144297952..144301828,4	K562	blood:
2	chr4:144292852..144297100-chr4:144298409..144302941,5	K562	blood:

Variant related genes	Relation type
GAB1	TF binding region
ENSG00000109458	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10017771	0.87[AFR][1000 genomes]
rs10023724	1.00[ASN][1000 genomes]
rs13104755	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13107986	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13116594	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13118809	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13127055	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13137712	0.81[AMR][1000 genomes]
rs17739332	1.00[ASN][1000 genomes]
rs28478042	0.87[AFR][1000 genomes]
rs28743166	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28925878	1.00[ASN][1000 genomes]
rs34234071	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34398038	0.81[AMR][1000 genomes]
rs34583666	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35027946	0.81[AMR][1000 genomes]
rs71610438	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610439	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610440	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71610442	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033347	chr4:144288438-144299563	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144272800-144299800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:144283000-144302200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:144284400-144299400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:144291000-144299800	Weak transcription	Pancreas	Pancrea
5	chr4:144291600-144299400	Weak transcription	Fetal Intestine Large	intestine
6	chr4:144291800-144302200	Weak transcription	Esophagus	oesophagus
7	chr4:144293200-144299400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr4:144293200-144299800	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr4:144293200-144302400	Enhancers	Brain Substantia Nigra	brain
10	chr4:144293600-144302000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:144294000-144302200	Weak transcription	Spleen	Spleen
12	chr4:144294000-144302400	Weak transcription	Gastric	stomach
13	chr4:144295000-144302800	Enhancers	Brain Cingulate Gyrus	brain
14	chr4:144295200-144301000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:144295200-144302400	Enhancers	Brain Anterior Caudate	brain
16	chr4:144295400-144299600	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr4:144295400-144300000	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr4:144295400-144300200	Enhancers	Fetal Brain Male	brain
19	chr4:144295400-144301000	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr4:144295400-144302000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr4:144295600-144300400	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr4:144295600-144300800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr4:144295600-144302400	Enhancers	Rectal Smooth Muscle	rectum
24	chr4:144295600-144303000	Enhancers	Brain Angular Gyrus	brain
25	chr4:144296000-144302200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:144296200-144299800	Weak transcription	Small Intestine	intestine
27	chr4:144296200-144302400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr4:144296600-144299400	Enhancers	Primary hematopoietic stem cells	blood
29	chr4:144296600-144299400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr4:144296600-144300000	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr4:144296600-144300200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:144296600-144300400	Enhancers	Adipose Nuclei	Adipose
33	chr4:144296600-144300600	Enhancers	Fetal Lung	lung
34	chr4:144296600-144301200	Enhancers	Primary B cells from peripheral blood	blood
35	chr4:144296800-144299400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr4:144296800-144299600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:144296800-144299800	Weak transcription	Lung	lung
38	chr4:144296800-144304600	Enhancers	Liver	Liver
39	chr4:144297000-144299400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:144297000-144299600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr4:144297000-144299800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr4:144297000-144301600	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:144297000-144302200	Weak transcription	Stomach Mucosa	stomach
44	chr4:144297000-144302600	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr4:144297200-144299400	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:144297200-144299400	Weak transcription	Fetal Intestine Small	intestine
47	chr4:144297200-144299400	Weak transcription	Osteobl	bone
48	chr4:144297200-144299800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:144297200-144299800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:144297200-144299800	Enhancers	Colon Smooth Muscle	Colon

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